BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089698.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 23,464,638 number of mapped reads = 17,254,213 (73.53%) number of supplementary alignments = 683 (0%) number of secondary alignments = 0 number of mapped bases = 787,711,272 bp number of sequenced bases = 787,546,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,480,928 duplication rate = 6.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8614 >>>>>>> ACTG content number of A's = 255,207,458 bp (32.41%) number of C's = 161,170,990 bp (20.46%) number of T's = 202,976,961 bp (25.77%) number of G's = 167,684,001 bp (21.29%) number of N's = 507,108 bp (0.06%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 4,419,170 number of insertions = 39,426 mapped reads with insertion percentage = 0.23% number of deletions = 111,036 mapped reads with deletion percentage = 0.64% homopolymer indels = 41.28% >>>>>>> Coverage mean coverageData = 0.2545X std coverageData = 1.3752X There is a 14.41% of reference with a coverageData >= 1X There is a 5.24% of reference with a coverageData >= 2X There is a 2.35% of reference with a coverageData >= 3X There is a 1.2% of reference with a coverageData >= 4X There is a 0.67% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 60055830 0.2409455581657307 1.520263406889685 chr2 243199373 70529503 0.29000692777279485 2.107721354542484 chr3 198022430 76979889 0.38874328024355626 1.130990763012923 chr4 191154276 30762741 0.16093148238023197 0.7008423179399395 chr5 180915260 34462916 0.19049203477915572 0.7116485394039177 chr6 171115067 51966445 0.30369298221997015 1.174078047032505 chr7 159138663 52545334 0.33018584553522357 2.2431084808968595 chr8 146364022 62440557 0.42661137721399867 2.5289768185962522 chr9 141213431 28434071 0.20135528751510895 1.205895045596731 chr10 135534747 33139732 0.2445109666231937 1.2730705878749233 chr11 135006516 37606264 0.2785514737673847 1.2486758444841812 chr12 133851895 27849807 0.20806434604455917 0.7784631661332855 chr13 115169878 23871874 0.2072753259320115 0.7542658966338945 chr14 107349540 27402651 0.25526565833444653 0.9508176103169323 chr15 102531392 20545239 0.2003799870385062 0.7350054919680382 chr16 90354753 15908378 0.17606575716055578 0.7886946202122906 chr17 81195210 18355620 0.22606776926865513 0.9115310487358866 chr18 78077248 39517180 0.5061292631625541 1.8722940212620813 chr19 59128983 13187003 0.22302096756847653 1.4617396410085721 chr20 63025520 17653999 0.28010874007862213 0.9439348764745483 chr21 48129895 12449798 0.25867079078398153 0.9929350171859097 chr22 51304566 6472638 0.12616105163037536 0.5735847255443434 chrMT 16571 165172 9.96753364311146 9.794261669282184 chrX 155270560 23570848 0.1518050041166851 1.0265331117743683 chrY 59373566 1837783 0.03095288229782257 0.5305099485142872